Merge pull request #1332 from Unidata/v4.6.3-dev-branch.wif

4.6.3 prep, upstream propegation

.travis.yml

@@ -37,4 +37,4 @@ before_install:
 
 script:
 
-    - docker run --rm -it -h "$CURHOST" -e USEDASH=FALSE -e RUNF=OFF -e RUNCXX=OFF -e RUNP=OFF -e RUNNCO=OFF -e USECMAKE=$USECMAKE -e USEAC=$USEAC -e DISTCHECK=$DISTCHECK -e COPTS="$COPTS" -e AC_OPTS="$AC_OPTS" -e CTEST_OUTPUT_ON_FAILURE=1 -v $(pwd):/netcdf-c -e USE_LOCAL_CP=$USECP -e TESTPROC=100  -e ENABLE_FILTER_TESTING=$TESTFILTER $DOCKIMG
+    - docker run --privileged --rm -it -h "$CURHOST" -e USEDASH=FALSE -e RUNF=OFF -e RUNCXX=OFF -e RUNP=OFF -e RUNNCO=OFF -e USECMAKE=$USECMAKE -e USEAC=$USEAC -e DISTCHECK=$DISTCHECK -e COPTS="$COPTS" -e AC_OPTS="$AC_OPTS" -e CTEST_OUTPUT_ON_FAILURE=1 -v $(pwd):/netcdf-c -e USE_LOCAL_CP=$USECP -e TESTPROC=100  -e ENABLE_FILTER_TESTING=$TESTFILTER -e ENABLE_C_MEMCHECK=OFF $DOCKIMG

CMakeLists.txt

@@ -26,13 +26,13 @@ set(PACKAGE "netCDF" CACHE STRING "")
 
 SET(NC_VERSION_MAJOR 4)
 SET(NC_VERSION_MINOR 6)
-SET(NC_VERSION_PATCH 3)
+SET(NC_VERSION_PATCH 4)
 SET(NC_VERSION_NOTE "-development")
 SET(netCDF_VERSION ${NC_VERSION_MAJOR}.${NC_VERSION_MINOR}.${NC_VERSION_PATCH}${NC_VERSION_NOTE})
 SET(VERSION ${netCDF_VERSION})
 SET(NC_VERSION ${netCDF_VERSION})
-SET(netCDF_LIB_VERSION 13)
-SET(netCDF_SO_VERSION 13)
+SET(netCDF_LIB_VERSION 15)
+SET(netCDF_SO_VERSION 15)
 SET(PACKAGE_VERSION ${VERSION})
 
 # Get system configuration, Use it to determine osname, os release, cpu. These
@@ -737,6 +737,8 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
 
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pset_libver_bounds "" HDF5_HAS_LIBVER_BOUNDS)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5free_memory "" HDF5_HAS_H5FREE)
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5allocate_memory "" HDF5_HAS_ALLOCATE_MEMORY)
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5resize_memory "" HDF5_HAS_RESIZE_MEMORY)
 
   IF(HDF5_PARALLEL)
 	SET(HDF5_CC h5pcc)
@@ -1845,7 +1847,7 @@ FOREACH(_LIB ${ALL_TLL_LIBS})
   LIST(APPEND LINKFLAGS "-L${_LIB_DIR}")
 ENDFOREACH()
 
-SET(NC_LIBS "-lnetcdf ${NC_LIBS}")
+#SET(NC_LIBS "-lnetcdf ${NC_LIBS}")
 
 STRING(REPLACE ";" " " NC_LIBS "${NC_LIBS}")
 STRING(REPLACE "-lhdf5::hdf5-shared" "-lhdf5" NC_LIBS ${NC_LIBS})
@@ -1859,6 +1861,9 @@ STRING(REPLACE ";" " " LINKFLAGS "${LINKFLAGS}")
 LIST(REMOVE_DUPLICATES NC_LIBS)
 LIST(REMOVE_DUPLICATES LINKFLAGS)
 
+SET(LIBS ${NC_LIBS})
+SET(NC_LIBS "-lnetcdf")
+
 configure_file(
   ${netCDF_SOURCE_DIR}/netcdf.pc.in
   ${netCDF_BINARY_DIR}/netcdf.pc @ONLY)
@@ -1919,10 +1924,6 @@ SET(LDFLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS_${CMAKE_BU
 is_disabled(BUILD_SHARED_LIBS enable_static)
 is_enabled(BUILD_SHARED_LIBS enable_shared)
 
-# Remove libnetcdf from NC_LIBS.
-STRING(REPLACE "-lnetcdf " "" TMP_NC_LIBS "${NC_LIBS}")
-SET(LIBS "${TMP_NC_LIBS}")
-
 is_enabled(ENABLE_V2_API HAS_NC2)
 is_enabled(ENABLE_NETCDF_4 HAS_NC4)
 is_enabled(ENABLE_HDF4 HAS_HDF4)

RELEASE_NOTES.md

@@ -5,15 +5,16 @@ Release Notes       {#RELEASE_NOTES}
 
 This file contains a high-level description of this package's evolution. Releases are in reverse chronological order (most recent first). Note that, as of netcdf 4.2, the `netcdf-c++` and `netcdf-fortran` libraries have been separated into their own libraries.
 
-## 4.6.3 - TBD
-
-## 4.6.2.1 - February 15, 2019
-
-### Maintenance Release
+## 4.6.3 - February 28, 2019
 
+* [Bug Fix] Correctly generated `netcdf.pc` generated either by `configure` or `cmake`.  If linking against a static netcdf, you would need to pass the `--static` argument to `pkg-config` in order to list all of the downstream dependencies.  See [Github #1324](https://github.com/Unidata/netcdf-c/issues/1324) for more information.
+* Now always write hidden coordinates attribute, which allows faster file opens when present. See [Github #1262](https://github.com/Unidata/netcdf-c/issues/1262) for more information.
+* Some fixes for rename, including fix for renumbering of varids after a rename (#1307), renaming var to dim without coordinate var. See [Github #1297](https://github.com/Unidata/netcdf-c/issues/1297).
+* Fix of NULL parameter causing segfaults in put_vars functions. See [Github #1265](https://github.com/Unidata/netcdf-c/issues/1265) for more information.
+* Fix of --enable-benchmark benchmark tests [Github #1211](https://github.com/Unidata/netcdf-c/issues/1211)
 * Update the license from the home-brewed NetCDF license to the standard 3-Clause BSD License.  This change does not result in any new restrictions; it is merely the adoption of a standard, well-known and well-understood license in place of the historic NetCDF license written at Unidata.  This is part of a broader push by Unidata to adopt modern, standardized licensing.  
 * [BugFix] Corrected DAP-releated issues on big-endian machines. See [Github #1321](https://github.com/Unidata/netcdf-c/issues/1321), [Github #1302](https://github.com/Unidata/netcdf-c/issues/1302) for more information.
-* [BugFix][Enhancement]  Various and sundry bugfixes and performance enhancements, thanks to @edhartnett, @gsjaardema, @t-b, @wkliao, and all of our other contributors.
+* [BugFix][Enhancement]  Various and sundry bugfixes and performance enhancements, thanks to \@edhartnett, \@gsjaardema, \@t-b, \@wkliao, and all of our other contributors.
 * [Enhancement] Extended `nccopy -F` syntax to support multiple variables with a single invocation. See [Github #1311](https://github.com/Unidata/netcdf-c/issues/1311) for more information.
 * [BugFix] Corrected an issue where DAP2 was incorrectly converting signed bytes, resulting in an erroneous error message under some circumstances. See [GitHub #1317](https://github.com/Unidata/netcdf-c/issues/1317) for more information.  See [Github #1319](https://github.com/Unidata/netcdf-c/issues/1319) for related information.
 * [BugFix][Enhancement] Modified `nccopy` so that `_NCProperties` is not copied over verbatim but is instead generated based on the version of `libnetcdf` used when copying the file.  Additionally, `_NCProperties` are displayed if/when associated with a netcdf3 file, now. See [GitHub #803](https://github.com/Unidata/netcdf-c/issues/803) for more information.

config.h.cmake.in

@@ -367,6 +367,12 @@ are set when opening a binary file on Windows. */
    nc4file. */
 #cmakedefine HDF5_HAS_H5FREE 1
 
+/* if true, H5allocate_memory() will be used. */
+#cmakedefine HDF5_HAS_ALLOCATE_MEMORY 1
+
+/* if true, H5resize_memory() will be used. */
+#cmakedefine HDF5_HAS_RESIZE_MEMORY 1
+
 /* if true, hdf5 has parallelism enabled */
 #cmakedefine HDF5_PARALLEL 1
 

configure.ac

@@ -13,7 +13,7 @@
 AC_PREREQ([2.59])
 
 # Initialize with name, version, and support email address.
-AC_INIT([netCDF], [4.6.3-development], [support-netcdf@unidata.ucar.edu], [netcdf-c])
+AC_INIT([netCDF], [4.6.4-development], [support-netcdf@unidata.ucar.edu], [netcdf-c])
 
 ##
 # Prefer an empty CFLAGS variable instead of the default -g -O2.
@@ -24,7 +24,7 @@ AC_INIT([netCDF], [4.6.3-development], [support-netcdf@unidata.ucar.edu], [netcd
 
 AC_SUBST([NC_VERSION_MAJOR]) NC_VERSION_MAJOR=4
 AC_SUBST([NC_VERSION_MINOR]) NC_VERSION_MINOR=6
-AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=3
+AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=4
 AC_SUBST([NC_VERSION_NOTE]) NC_VERSION_NOTE="-development"
 
 #####
@@ -1028,7 +1028,7 @@ if test "x$enable_hdf5" = xyes; then
 
    # H5Pset_fapl_mpiposix and H5Pget_fapl_mpiposix have been removed since HDF5 1.8.12.
    # Use H5Pset_fapl_mpio and H5Pget_fapl_mpio, instead.
-   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
+   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5resize_memory H5allocate_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
 
    # Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
    if test "x$ac_cv_func_H5Pset_all_coll_metadata_ops" = xyes; then
@@ -1062,6 +1062,14 @@ if test "x$enable_hdf5" = xyes; then
       AC_DEFINE([HDF5_HAS_H5FREE], [1], [if true, H5free_memory() will be used to free hdf5-allocated memory in nc4file.])
    fi
 
+   if test "x$ac_cv_func_H5allocate_memory" = xyes; then
+      AC_DEFINE([HDF5_HAS_ALLOCATE_MEMORY], [1], [if true, H5allocate_memory() will be used.])
+   fi
+
+   if test "x$ac_cv_func_H5resize_memory" = xyes; then
+      AC_DEFINE([HDF5_HAS_resize_MEMORY], [1], [if true, H5resize_memory() will be used.])
+   fi
+
    if test "x$ac_cv_func_H5Pset_libver_bounds" = xyes; then
       AC_DEFINE([HDF5_HAS_LIBVER_BOUNDS], [1], [if true, netcdf4 file properties will be set using H5Pset_libver_bounds])
    fi

docs/Doxyfile.developer

@@ -38,7 +38,7 @@ PROJECT_NAME           = netCDF-C
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.6.3-development
+PROJECT_NUMBER         = 4.6.4-development
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

docs/guide.dox

@@ -8,7 +8,6 @@
 - \subpage netcdf_data_set_components
 - \subpage netcdf_perf_chunking
 - \subpage netcdf_utilities_guide
-- \subpage compress
 - \subpage BestPractices
 - \subpage user_defined_formats
 - \subpage users_guide_appendices
@@ -48,7 +47,10 @@ web site (http://www.unidata.ucar.edu/netcdf), and with the netCDF
 distribution.
 
 The latest version of this document, and the language specific guides,
-can be found at the netCDF web site (http://www.unidata.ucar.edu/netcdf/docs) along with extensive additional information about netCDF, including pointers to other software that works with netCDF data.
+can be found at the netCDF web site
+(http://www.unidata.ucar.edu/netcdf/docs) along with extensive
+additional information about netCDF, including pointers to other
+software that works with netCDF data.
 
 Separate documentation of the Java netCDF library can be found at
 http://www.unidata.ucar.edu/software/netcdf-java/.
@@ -88,8 +90,10 @@ were written.
 
 Unidata supports the netCDF interfaces for C (see <a
 href="http://www.unidata.ucar.edu/netcdf/docs/" >NetCDF-C User's
-Guide</a>), Fortran (see <a href="http://www.unidata.ucar.edu/netcdf/fortran/docs/" >NetCDF-Fortran User's Guide</a>)
-and C++ (see <a href="http://www.unidata.ucar.edu/netcdf/documentation/historic/cxx4/index.html"
+Guide</a>), Fortran (see <a
+href="http://www.unidata.ucar.edu/netcdf/fortran/docs/"
+>NetCDF-Fortran User's Guide</a>) and C++ (see <a
+href="http://www.unidata.ucar.edu/netcdf/documentation/historic/cxx4/index.html"
 >NetCDF C++ Interface Guide</a>).
 
 The netCDF library is supported for various UNIX operating systems. A